The overall goal of our research is to develop a deeper understanding of the genetic factors underlying dyslipidemia and atherosclerosis. Areas of complex blood flow develop plaques preferentially, and the influence of hemodynamics on plaque development has been discussed extensively. Evidence is also accumulating that atherosclerosis at different vascular locations can involve distinguishable risk factors, although little attention has been paid to genetic factors that influence the sites of plaque development. We have found that Apoe-/- mice with the 129S6 genetic background (129-apoE) are slower to develop plaques at the aortic root than are Apoe-/- mice with a C57BL/6J background (B6-apoE), yet the 129-apoE mice develop plaques more rapidly in the aortic arch. Our quantitative trait loci (QTL) mapping of an F2 population of Apoe-/- mice between these strains has identified two QTL peaks, Aa1 and Aa2 on chromosome 1, that influence the susceptibility of the aortic arch to develop lesions. QTL-Aa1 overlaps QTL-Ga1, a QTL that influences the geometry of aortic arch curvature. The aortic arch QTLs are distinct from those affecting aortic root lesions. These observations support our hypothesis that subtle differences in vessel formation during development influence the occurrence of atherosclerosis later in life. Specific Aim 1 will further refine the QTL-Aa1 and Aa2 maps using genetic crosses, congenics and genome comparisons of inbred strains, 129S6, C57BL6/J, DBA/2J, A/J and AKR. Specific Aim 2 will facilitate targeted crossover within QTL intervals. Identifying the genes that form a QTL is facilitated when a congenic region is subdivided by crossover during backcrossing. To accelerate this process, we will combine meiosis-specific expression of I-SceI, a homing endonuclease of yeast, with its recognition sequence inserted into candidate genes within the QTL regions. The atherogenic effects of the induced mutations and of the narrowed QTL intervals will be assessed on an apoE-null background. Specific Aim 3 will test whether variations in the Gli2 gene influence aortic arch geometry and atherosclerosis. Gli2 lies within the interval covered by our overlapping QTLs, Aa1 and Ga1, and it codes for a transcriptional factor that mediates the sonic hedgehog signaling important for many developmental processes, including remodeling of branchial arch blood vessels to form the aortic arch. Deciphering genetic factors that affect plaque initiation and growth at one location along the aorta but not at another location has direct clinical relevance. Gaining a better understanding of location-dependent plaque development is an important contribution to the long-term goal of preventing the disease or of treating it before it becomes life threatening.